I think "Spectre of the Gun" could be said to have some funny moments, especially with Chekhov, and the whole "fish out of water" aspect of our heroes in this weird Melkotion trap. And "Day of the Dove" ends lightheartedly and with some humor, at least (Kang slapping Kirk very hard on the back).

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All universes will be assimilated. Resistance is futile---JJ "The Borg" Abrams